diff --git a/bin/gstack-gbrain-detect b/bin/gstack-gbrain-detect
index e79f4d558..1f9d1140a 100755
--- a/bin/gstack-gbrain-detect
+++ b/bin/gstack-gbrain-detect
@@ -27,13 +27,19 @@
  * gbrain_local_status. Key order may differ from the bash version's `jq -n`
  * output — downstream parsers must not depend on key order (none currently do).
  *
+ * Flags:
+ *   --is-ok   exit 0 iff the local engine is usable (see below).
+ *   --doctor  run `gbrain doctor --json --scope=brain` and print
+ *             {brain_ok, status, brain_failures, skill_failures, report};
+ *             exit 0 iff brain_ok. Skill checks never decide brain_ok (#3790).
+ *
  * Env:
  *   GSTACK_HOME      — override ~/.gstack for state lookups (used by tests).
  *   HOME             — effective user home (drives ~/.gbrain/config.json path).
  *   GSTACK_DETECT_NO_CACHE=1 — bypass the 60s local-status cache.
  */
 
-import { execFileSync } from "child_process";
+import { execFileSync, spawnSync } from "child_process";
 import { existsSync, readFileSync } from "fs";
 import { homedir } from "os";
 import { join } from "path";
@@ -118,21 +124,57 @@ function detectPoolerMode(): "transaction" | "session" | "unknown" | null {
   return isTransactionModePooler(parsed.database_url) ? "transaction" : "session";
 }
 
-// --- gbrain doctor health (any nonzero exit or non-"ok"/"warnings" status → false) ---
+// --- gbrain doctor health, judged from brain checks only (#3790) ---
 //
+// gbrain doctor's skill checks (category "skill": resolver_health,
+// skill_conformance, ...) grade whatever skills dir gbrain auto-detects, which
+// can be another agent's workspace such as ~/.openclaw/workspace. They say
+// nothing about the brain, so they never decide health here. `--scope=brain`
+// (gbrain v0.41.20+) skips that group; older gbrain ignores the flag, so
+// failed checks tagged "skill" are dropped as well. gbrain's status is
+// "healthy"/"warnings"/"unhealthy"; "ok" is kept for older reports. doctor
+// exits 1 when any check fails, so stdout is read whatever the exit code.
+interface DoctorVerdict {
+  brain_ok: boolean;
+  status: string | null;
+  brain_failures: string[];
+  skill_failures: string[];
+  report: unknown;
+}
+
+function runDoctor(extraArgs: string[], timeoutMs: number): DoctorVerdict {
+  const r = spawnSync("gbrain", ["doctor", "--json", ...extraArgs, "--scope=brain"], {
+    encoding: "utf-8",
+    timeout: timeoutMs,
+    stdio: ["ignore", "pipe", "ignore"],
+  });
+  let report: { status?: string; checks?: { name?: string; status?: string; category?: string }[] } | null = null;
+  try {
+    report = JSON.parse(r.stdout || "null");
+  } catch {}
+  if (!report || typeof report !== "object") {
+    return { brain_ok: false, status: null, brain_failures: [], skill_failures: [], report: null };
+  }
+  const failed = (Array.isArray(report.checks) ? report.checks : []).filter((c) => c?.status === "fail");
+  const skill_failures = failed.filter((c) => c.category === "skill").map((c) => c.name ?? "unnamed");
+  const brain_failures = failed.filter((c) => c.category !== "skill").map((c) => c.name ?? "unnamed");
+  const status = report.status ?? null;
+  const statusOk = status === "healthy" || status === "ok" || status === "warnings";
+  return {
+    brain_ok: brain_failures.length === 0 && (statusOk || skill_failures.length > 0),
+    status,
+    brain_failures,
+    skill_failures,
+    report,
+  };
+}
+
 // Uses --fast to avoid hanging on a dead DB. Per the local-status classifier
 // (which probes DB directly via `gbrain sources list`), gbrain_doctor_ok is a
 // coarse health summary, not engine-reachability — that's gbrain_local_status.
 function detectDoctor(onPath: boolean): boolean {
   if (!onPath) return false;
-  const out = tryExec("gbrain", ["doctor", "--json", "--fast"], 3_000);
-  if (!out) return false;
-  try {
-    const parsed = JSON.parse(out) as { status?: string };
-    return parsed.status === "ok" || parsed.status === "warnings";
-  } catch {
-    return false;
-  }
+  return runDoctor(["--fast"], 3_000).brain_ok;
 }
 
 // --- artifacts sync mode ---
@@ -300,6 +342,14 @@ function main(): void {
 // callers — setup, bin/dev-setup, and `gstack-config gbrain-refresh` — can
 // decide whether to render the gbrain :user variant without duplicating the
 // JSON grep. Prints nothing on stdout.
+// --doctor: the full brain-health gate /setup-gbrain Step 5 runs. Prints the
+// DoctorVerdict as JSON and exits 0 iff brain_ok.
+if (process.argv.includes("--doctor")) {
+  const verdict = runDoctor([], 120_000);
+  process.stdout.write(JSON.stringify(verdict, null, 2) + "\n");
+  process.exit(verdict.brain_ok ? 0 : 1);
+}
+
 if (process.argv.includes("--is-ok")) {
   const noCache = process.env.GSTACK_DETECT_NO_CACHE === "1";
   const status = localEngineStatus({ noCache });
diff --git a/setup-gbrain/SKILL.md b/setup-gbrain/SKILL.md
index 201c54af9..6f6d785ea 100644
--- a/setup-gbrain/SKILL.md
+++ b/setup-gbrain/SKILL.md
@@ -315,12 +315,14 @@ compatible MCP version.
 For Paths 1, 2a, 2b, 3, switch:
 
 ```bash
-doctor=$(gbrain doctor --json)
-status=$(echo "$doctor" | jq -r .status)
+DOCTOR=$(~/.claude/skills/gstack/bin/gstack-gbrain-detect --doctor)
+BRAIN_OK=$(echo "$DOCTOR" | jq -r .brain_ok)
 ```
 
-If status is `ok` or `warnings`, proceed. Anything else → surface the full
-doctor output and STOP.
+If `BRAIN_OK` is `true`, proceed; only brain checks count. Note any
+`skill_failures`: gbrain graded a skills dir it found, maybe another agent's
+(`~/.openclaw/workspace`). Never edit that workspace to pass. Otherwise show
+`echo "$DOCTOR" | jq .report` and STOP.
 
 ---
 
diff --git a/setup-gbrain/SKILL.md.tmpl b/setup-gbrain/SKILL.md.tmpl
index 02c0f096a..4de37a6b9 100644
--- a/setup-gbrain/SKILL.md.tmpl
+++ b/setup-gbrain/SKILL.md.tmpl
@@ -230,12 +230,14 @@ compatible MCP version.
 For Paths 1, 2a, 2b, 3, switch:
 
 ```bash
-doctor=$(gbrain doctor --json)
-status=$(echo "$doctor" | jq -r .status)
+DOCTOR=$(~/.claude/skills/gstack/bin/gstack-gbrain-detect --doctor)
+BRAIN_OK=$(echo "$DOCTOR" | jq -r .brain_ok)
 ```
 
-If status is `ok` or `warnings`, proceed. Anything else → surface the full
-doctor output and STOP.
+If `BRAIN_OK` is `true`, proceed; only brain checks count. Note any
+`skill_failures`: gbrain graded a skills dir it found, maybe another agent's
+(`~/.openclaw/workspace`). Never edit that workspace to pass. Otherwise show
+`echo "$DOCTOR" | jq .report` and STOP.
 
 ---
 
diff --git a/test/setup-gbrain-doctor-gate.test.ts b/test/setup-gbrain-doctor-gate.test.ts
new file mode 100644
index 000000000..8137cf1d4
--- /dev/null
+++ b/test/setup-gbrain-doctor-gate.test.ts
@@ -0,0 +1,131 @@
+/**
+ * /setup-gbrain Step 5 and gstack-gbrain-detect judge brain health from brain
+ * checks only (#3790).
+ *
+ * gbrain doctor's skill checks (category "skill": resolver_health,
+ * skill_conformance, ...) grade whatever skills dir gbrain auto-detects, which
+ * can be another agent's workspace such as ~/.openclaw/workspace. A failure
+ * there made a working brain read "unhealthy", Step 5 stopped, and the agent
+ * proposed editing the other agent's workspace. Real brain failures
+ * (connection, schema_version, pgvector) must still stop Step 5.
+ *
+ * A stub gbrain on PATH serves canned doctor JSON; no real gbrain runs.
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { spawnSync } from 'child_process';
+
+const ROOT = path.resolve(import.meta.dir, '..');
+const DETECT = path.join(ROOT, 'bin', 'gstack-gbrain-detect');
+const SKILL_MD = path.join(ROOT, 'setup-gbrain', 'SKILL.md');
+
+const check = (name: string, category: string, status = 'ok') => ({ name, category, status, message: '' });
+const BRAIN_OK = [
+  check('connection', 'ops'), check('pgvector', 'ops'), check('schema_version', 'meta'), check('embeddings', 'brain'),
+];
+const SKILL_FAIL = check('resolver_health', 'skill', 'fail');
+const report = (checks: ReturnType<typeof check>[]) => ({
+  schema_version: 2,
+  status: checks.some((c) => c.status === 'fail') ? 'unhealthy' : checks.some((c) => c.status === 'warn') ? 'warnings' : 'healthy',
+  checks,
+});
+const withFailure = (name: string) => BRAIN_OK.map((c) => (c.name === name ? { ...c, status: 'fail' } : c));
+
+type Case = { full: object; scoped: object };
+const CASES: Record<string, Case> = {
+  // gbrain >= v0.41.20: --scope=brain drops the skill group.
+  'skill-only failure': {
+    full: report([...BRAIN_OK, SKILL_FAIL]),
+    scoped: report([...BRAIN_OK, check('harness_wiring', 'ops', 'warn')]),
+  },
+  // Older gbrain ignores --scope=brain and still runs the skill group.
+  'skill-only failure, gbrain without --scope': {
+    full: report([...BRAIN_OK, SKILL_FAIL]),
+    scoped: report([...BRAIN_OK, SKILL_FAIL]),
+  },
+  'all checks pass': { full: report(BRAIN_OK), scoped: report(BRAIN_OK) },
+  'connection failure': { full: report([...withFailure('connection'), SKILL_FAIL]), scoped: report(withFailure('connection')) },
+  'schema_version failure': { full: report([...withFailure('schema_version'), SKILL_FAIL]), scoped: report(withFailure('schema_version')) },
+  'pgvector failure': { full: report([...withFailure('pgvector'), SKILL_FAIL]), scoped: report(withFailure('pgvector')) },
+  'pgvector failure, gbrain without --scope': {
+    full: report([...withFailure('pgvector'), SKILL_FAIL]),
+    scoped: report([...withFailure('pgvector'), SKILL_FAIL]),
+  },
+};
+const HEALTHY = ['skill-only failure', 'skill-only failure, gbrain without --scope', 'all checks pass'];
+
+let tmp: string;
+const SAFE_PATH = '/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin';
+
+beforeAll(() => {
+  tmp = fs.mkdtempSync(path.join(os.tmpdir(), 'gbrain-doctor-gate-'));
+  fs.mkdirSync(path.join(tmp, 'bin'));
+  fs.symlinkSync(process.execPath, path.join(tmp, 'bin', 'bun'));
+  // gbrain doctor exits 1 when any check fails and prints the report anyway.
+  fs.writeFileSync(path.join(tmp, 'bin', 'gbrain'), `#!/bin/sh
+case "$1" in
+  --version) echo "gbrain 0.60.537.0"; exit 0 ;;
+  doctor) ;;
+  *) exit 2 ;;
+esac
+f="$FAKE_DOCTOR_DIR/full.json"
+for a in "$@"; do [ "$a" = "--scope=brain" ] && f="$FAKE_DOCTOR_DIR/scoped.json"; done
+cat "$f"
+grep -q '"status":"unhealthy"' "$f" && exit 1
+exit 0
+`, { mode: 0o755 });
+});
+
+afterAll(() => fs.rmSync(tmp, { recursive: true, force: true }));
+
+function caseEnv(name: string) {
+  const dir = path.join(tmp, name.replace(/[^a-z0-9]+/gi, '-'));
+  fs.mkdirSync(path.join(dir, 'home'), { recursive: true });
+  fs.writeFileSync(path.join(dir, 'full.json'), JSON.stringify(CASES[name]!.full));
+  fs.writeFileSync(path.join(dir, 'scoped.json'), JSON.stringify(CASES[name]!.scoped));
+  return {
+    ...process.env,
+    PATH: `${path.join(tmp, 'bin')}:${SAFE_PATH}`,
+    HOME: path.join(dir, 'home'),
+    GSTACK_HOME: path.join(dir, 'state'),
+    GSTACK_DETECT_NO_CACHE: '1',
+    FAKE_DOCTOR_DIR: dir,
+  };
+}
+
+function step5Fence(): string {
+  const md = fs.readFileSync(SKILL_MD, 'utf-8');
+  const start = md.indexOf('## Step 5: Verify gbrain doctor');
+  const end = md.indexOf('\n## ', start + 1);
+  expect(start).toBeGreaterThan(-1);
+  const fence = md.slice(start, end).match(/\`\`\`bash\n([\s\S]*?)\`\`\`/);
+  expect(fence).not.toBeNull();
+  return fence![1]!.replaceAll('~/.claude/skills/gstack/bin/', `${ROOT}/bin/`);
+}
+
+describe('/setup-gbrain Step 5 doctor gate', () => {
+  for (const name of Object.keys(CASES)) {
+    const healthy = HEALTHY.includes(name);
+    test(`${name}: Step 5 ${healthy ? 'proceeds' : 'stops'}`, () => {
+      const r = spawnSync('bash', ['-c', `${step5Fence()}\necho "BRAIN_OK=\${BRAIN_OK:-unset} status=\${status:-unset}"`], {
+        env: caseEnv(name), encoding: 'utf-8', timeout: 30_000,
+      });
+      const verdict = r.stdout.trim().split('\n').pop();
+      expect(verdict).toStartWith(`BRAIN_OK=${healthy}`);
+    });
+  }
+});
+
+describe('gstack-gbrain-detect gbrain_doctor_ok', () => {
+  for (const name of Object.keys(CASES)) {
+    const healthy = HEALTHY.includes(name);
+    test(`${name}: gbrain_doctor_ok is ${healthy}`, () => {
+      const r = spawnSync(DETECT, [], { env: caseEnv(name), encoding: 'utf-8', timeout: 30_000 });
+      expect(r.status).toBe(0);
+      expect(JSON.parse(r.stdout).gbrain_doctor_ok).toBe(healthy);
+    });
+  }
+});